User Manual - People - Kansas State University
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1. 4 Further analyses Te Functional annotations using blast2GO Signal peptide predictions E from ORFs at least 30 bases Standard genetic code imi nucleotides between STOP codons Y Reset form to default values Internet Protected Mode On Page 15 User Manual Version 1 0 Figure 1 Request submission Web Page of ArthropodEST pipeline system First users must enter the project name an email address to receive notification about results and an input EST file After that they must select at least one of the possible analysis operations shown in the web page Every operation is linked to one correspondent Bioinformatics Software They may choose appropriate parameters for each option according their necessities The reference about the programs to be launched for EST analysis is described at the bottom of the web page Users are supposed to understand the analysis operations for their EST input files Finally users press Submit for EST analysis button and wait for being notified by email when results are ready After a request is placed if Beocat has available resources and currently there are not running the maximum number of allowed executions the engine will submit correspondent jobs to the cluster and a first email notification is sent to user to determine the analysis has begun Notice that even the process was already sent to2. Upload EST file plain text FASTA sequences EE Upload corresponding Leen scores Vus file C Temp file fsa Browse 1 m Sequence trimming cleaning vector and contaminant screening Seaclean program manual Min length to consider sequence valid 100 F Vector screening with NCBI UniVec Core and EMBL EmVec I Trash low quality sequences Low complexity dust screening e Trim ends rich in undetermined bases N s re Trim polyA tails I Upload your own men file end FASTA sequences Optional Upload your own file pense FASTA sequences RepeatMasking Select closest species clade of your ESTs repetitive regions in lowercase rather than N S lowercase not recommended if you are using TGICL TORRES below 3 Usage section in TGICL program manual Contig assembly with optional prior clustering the default values below need to be fine tuned for your data set E Clustering TGICL program manual Min 96 identity for overlap 94 1 Base pairs for overlap 30 Max length unmatched overhangs 800 Contig assembly CAP3 program manual Base quality cutoff value for clipping gt 5 Max gap length in any overlap gt 1 Overlap length cutoff 15 40 Overlap 96 identity cutoff gt 65 Overlap similarity score cutoff gt 250 Clipping range gt 5 Max overhang 96 length 2 Max number word matches gt 30 300 Min number good reads at clip pos gt 0
3. User Manual for ArthropodEST pipeline System Version 1 0 Submitted in partial fulfillment of the requirements of the degree of Master of Software Engineering Prepared by Luis Fernando Carranco M CIS 895 MSE Project Kansas State University Spring 2010 Table of Contents L introductio No e sneller 6 2 Installation and Configuration seesi a aea 6 2 1 Bioinformatics EE 6 2 1 1 Required SOftWAFe iiti a ee die tee itn 6 2 1 2 Database x cest ehe telae handy Be aee e ka ke ka e e Ne ed a 7 2 1 3 Engine coordinatore e eet oe envie tetti ten 7 2 1 4 Web Interface iiie RR RE ER RERO ERBRINGEN RE a E ERES es 10 2 2 Beocat Cluster Server tre t ER ER EE ere Ou RIEN HERR RE eren 11 2 2 1 Event Log component EE 12 2 2 2 Bioinformatics SOftWale occi cette pos ett et ee PRENNE EE CERE ERE Ea a NY NEAR ERE an EP Di n steds 12 2 2 3 lt el le gl EE 13 3 ArthropodEST Pipeline Usage gege a e er dad fos 14 3 1 User IN Ee 14 3 1 1 SUBMIT NW UE 15 3 1 2 Monitor Request EE 16 3 1 3 Cancel Request s rasler 17 3 1 4 View Request Results i tre as 18 3 2 tellt Del TEE 19 3 2 1 Login danses som ae See O 20 3 2 2 L t ES 20 3 2 3 Change PassWOFd enee see te Em t te emer ev pet ER 20 3 2 4 RES OUNCES m 21 3 2 5 e Le 22 3 2 6 Analysis Request Detail 24 3 2 7 3 2 8 3 2 9 Cancel Requests cccscccccceeeeeees View Request Results Start and Stop Engine coordinator Table of Figu
4. It is important to notice that it might be installed on a separated machine as a dedicated server Below are the steps to set up a database MySQL root user must perform the installation 2 1 3 Create a database for ArthropodEST Pipeline system CREATE DATABASE arthropodest Create a user with permissions to access the database from BC server and Beocat Their IP addresses are needed for set up this CREATE USER arthropodest bcserverip IDENTIFIED BY athropodestpass CREATE USER arthropodest beocatip IDENTIFIED BY athropodestpass GRANT SELECT INSERT UPDATE DELETE TRIGGER USER ON arthropodest TO arthropodest G bcserverip GRANT SELECT INSERT UPDATE DELETE TRIGGER USER ON arthropodest TO arthropodest G beocat Create database structure Use the schema sq file provided on the system package mysql uroot ppassroot hlocalhost P 3306 dbName path to schema sql Engine coordinator The engine coordinator is a service coded in python and it runs as a Unix daemon It must be launched as a root because the service later on will automatically drop privileges to run as the apache Page 7 User Manual Version 1 0 user www data The following are the steps to set up the engine Root user must perform the installation e Unpack the engine source code in a desired lo
5. queueLength STRING var www e log queue_le ngth Path to the file that will content the number of current request being processed Page 9 User Manual Version 1 0 daemon stdout STRING tmp est out Path to the file where engine stdout will be redirected dev null by default daemon stderr STRING tmp est err Path to the file where engine stderr will be redirected dev null by default daemon_pidfile STRING tmp est pid Path to the file that will hold the engine process id This will be present while engine running e Table 1 Configuration file engine est cfg Logging configuration file establishes how the engine coordinator will log the events generated during the processing of a request For more information how to add more handlers and change format of output refer python documentation http docs python org library logging html There are two loggers used by the application Engine and Paramiko Log Handlers The recommended parameters that might be changed are listed on the table below Section Parameter Format Default Description Name Example logger engine est level STRING INFO Level of messages to be logged DEBUG INFO ERROR handlers STRING fileHandler Handlers used to manage engine log messages logger paramiko level STRING ERROR Level of messages to be logged DEBUG INFO ERROR handlers STRING fileHandler pa Handlers used to manage paramiko library lo
6. 04 15 2010 22 30 49 CANCELLED info ecuadorhost com test6 april15 04 15 2010 22 30 56 DONE info ecuadorhost com test7 april15 04 15 2010 22 31 03 DONE info ecuadorhost com Oo Ol NL OD als VIN test8 april15 04 15 2010 22 31 09 DONE info ecuadorhost com o jo o o o o o o o o o test9 april15 04 15 2010 22 31 17 DONE info ecuadorhost com num rows 10 gt gt gt page number 1 Done Internet Protected Mode On Figure 8 Reports Web Page Administration Interface 3 2 6 Analysis Request Detail The analysis requests detail section shows the complete information about a particular request The following figure shows the Web Page with the distribution of the information for one request Page 24 User Manual Version 1 0 File Edit View History Bookmarks Tools Help QU X 4 E http 129 130115 77 e2 beocat admin viewjob php id 86 A AA Google ArthropodEST K State Bioinformatics EST analysis pipeline Logout Change Pass Resources Reports Request Input File s Project test large april18 Lx info ecuadorhost com Size T Filename bp bytes poe p 04 18 2010 10 01 45 benchmark10000 seq 5501584 mr Jen n ur arguments d arthropodest tmpitest large april18 9g1J1X40d6Qg5 o arthropodest Irftest large april18 91J1X40d6Qg5 e info ecuadorhost com P test large april18 F benchm
7. Beocat the execution can be delayed by Beocat scheduler because it might be very busy with no nodes available to start the execution 3 1 2 Monitor Request The first notification email will include a URL to a web page so that users may monitor or cancel the analysis request The URL will include a unique identifier correspondent to particular request For Users might monitor their requests opening that web page on a browser The status of the selected analysis operations will be shown in a detailed table Figure 2 shows a screen shot with a request that was recently placed and waiting to be executed The Refresh Information button allows user reloads the page to show the latest information regarding the status of the analysis request Page 16 User Manual Version 1 0 E ArthropodEST Job status Windows Internet Explore 4 R http 129 130 115 77 e2 beocat myjob php Ly Favorites ArthropodEST K State Bioinformatics EST analysis pipeline Project name my project Number of sequences 11 Status CREATED Refresh information Analysis step Start Time End Time Sequence trimming RepeatMasking Contig Clustering Signal peptide predictions Annotations blast2GO Internet Protected Mode On i Figure 2 Monitor a request Web Page of ArthropodEST pipeline system 3 1 3 Cancel Request On the status page if a request is pro
8. User Manual Version 1 0 allowed Then if the current percentage is less or equal than the threshold configured it will allocate the maximum values Otherwise the minimum values will be used to allocate the request For more information about configuration parameters look at configuration engine file at section 2 3 1 l S ArthropodES Resources Windows Interne Explore Lo mes e R http 129 130 115 77 e2 beocat admin resources php 7 BAA 9 Google Ari BB E Arthrop EE Arthr x m ta v v 7 de v Pager Safetyv Toolsv v ArthropodEST K State Bioinformatics EST analysis pipeline Logout Change Pass Resources Reports ScriptiD Hour Cpus Memory Cpus Memory 1 1 00 00 1 1G 0 00 1 G i delete 2 2 00 00 2 3 0 00 1 G i delete delete delete delete 0 00 2 1G 3 00 00 6 i delete 10 00 00 G 0 00 G i delete 10 00 00 3 0 00 00 G i delete 5000 3 3 00 00 1 3 3 00 00 G i delete Internet Protected Mode On Figure 7 Resource Web Page Administration Interface 3 2 5 Reports This administration section is intended to retrieve from MySQL database the analysis re
9. aphid ests raw txt clean masked cap singlets gz 21 Apr 2010 0021 376 P pea aphid ests raw txt clean masked gz 21 Apr 2010 0021 1 3K D pea aphid ests raw txt clean out gz 21 Apr 2010 0021 251 P pea aphid ests raw txt clean tbl gz 21 Apr 2010 0021 798 dh pea aphid ests raw txt cln gz 21 Apr 2010 0021 366 Internet Protected Mode On Figure 4 Results Web Page of ArthropodEST pipeline system 3 2 Administrator Interface The purpose of this section is to provide a guide to administrator s about how they must interact with the ArthropodEST Pipeline system to perform management activities Page 19 User Manual Version 1 0 3 2 1 Login The login web page is intended to authenticate the administrator user before using the administrator Web Pages User must enter the username admin and the correspondent password The default password is admin ArthropodEST K State Bioinformatics EST analysis pipeline Administrator Login Username admin Password eeeee Login Internet Protected Mode On Figure 5 Login Web Page Administration Interface 3 2 2 Logout When the administrator was authenticated he or she can exit from the session using the logout link provided on the administrator interface at the left top The administrator might logout any time during the administration activities If the administrator does not do anything during 15 minutes the session will automatically expire T
10. software and event log component are installed Modify the following lines of code as necessa ry WWW HOST URL 2 http 129 130 115 77 e2 beocat LOG arthropodest src log est py Event log component WWW EST LOG DIR arthropodest log full PATH of log directory Location Bioinformatics Software SCRIPTS arthropodest bin a EQSTATS_WORKDIR arthropodest tmp CBI_UNIVEC bioinfo_software vectors ncbi_univec UniVec_Cor EMBL EMVEC bioinfo software vectors embl emvec emvec dat fsa FORMATDB bioinfo software ncbi blast bin formatdb SEQCL bioinfo software tgi seqclean seqclean Page 13 User Manual Version 1 0 CLN2QUAL bioinfo_software tgi seqclean cln2qual CDBYANK bioinfo_software tgi seqclean bin cdbyank REPMASK bioinfo_software RepeatMasker RepeatMasker TGICL bioinfo_software tgi tgicl_linux tgicl CAP 3 bioinfo_software cap3 cap3 BLASTX homes bioinfo bioinfo_software ncbi blast netblast bin blastcl3 p blastx d nr BLASTX PARAMS 1 04 m 7 b 20 v 20 JAVA usr bin java JAVA OPTS client Xms64m Xmx512m BLAST2GO S JAVA S JAVA OPTS jar homes bioinfo bioinfo software blast2go blast2go jar prop homes bioinfo bioinfo software blast2go b2gPipe properties BLAST2GO_PARAMS a d AWK usr bin awk PYTHON usr bin python SET PATH FOR RUNNING ON BEOCAT NODES ArthropodEST PATH bioinfo software bioinf
11. ark10000 seq S l 100 V r drosophila A 1 O c 12 20 o 40 p 90 s 900 y 100 h 20 300 z 3 p 1 B 1 e seqcl repmask sh Project name test large april18 e seqcl repmask sh User email info ecusdorhost com e seqolrepmask sh Input EST file benchmark10000 seq e seqcl repmask sh Input EST qual scores file amp e seqcl repmask sh User vectors file e seqcl repmask sh User contaminants file e seqcl repmask sh Seqclean options v homes bicinfo bicinfo software vectors ncbi univec UniVec Core homes bicinfo bioinfo software vectors embl emvec emvec dat fsa 1 100 more gt gt basses sus seus Santino etme Bon Se ener someon EE aman ms ez men jene e ja eeng re oon oec armor erez we JL EEE E E EECHER ETA O E E s JL View results Done Figure 9 Request Detail Web Page Administration Interface The section Request Data consists of the main information regarding the analysis requests The Request Input File s section shows the input file s provided to perform the analysis The table at the bottom shows its operations and the status of their execution They include complete information about Page 25 User Manual Version 1 0 every execution including start and end time duration number of CPUs used by Beocat and an error message if any produced while executing pipeline scripts 3 2 7 Cancel Requests During the execution of a request the Administrator is able to canc
12. cation on server e Grant read and write permissions only for root user to configurations files engine est cgf and engine logging cfg e Modify configuration files according the parameters specified in tables below Notice that configuration files follows the python convention grouping parameters entries name value in sections headers section http docs python org library configparser html Do not change parameter or section names on those files but values according necessities Section Parameter Name Format Default Example Description MySql host STRING localhost Database host name might be IP address port INT 3306 Database connection port user STRING dbuser Database user name password STRING dbpassword Database password db STRING dbname Database name Beocat host STRING beocat cis ks u edu Beocat host name might be IP address user STRING bioinfo Beocat user account where pipeline components resides password STRING Beocat user password This argument is optional if a private key is used to authenticate rsa_file STRING home id_rsa Local absolute path where private key of Beocat user is located If specified the correspondent public key must Beocat account file be included on user ssh authorized_keys rsa_password STRING If the private key provided is encrypted the pass
13. cessing it will appear a Cancel Request button that allow users to cancel the request execution After pressing the button a message will appear so that users confirm that they actually want to cancel the request After cancelling a notification will be sent to user to indicate that the request was successfully cancelled The following screen shot shows an executing request that might be cancelled Page 17 User Manual Version 1 0 a Google me w Page v Safety v Tools v r ArthropodEST K State Bioinformatics EST analysis pipeline Project name myproject Number of sequences 515 Status SUBMITTED Refresh information Cancel EST analysis Analysis step Status Start Time End Time Sequence trimming DONE 04 21 2010 01 08 45 04 21 2010 01 08 58 RepeatMasking RUNNING 04 21 2010 01 08 58 Contig Clustering WAITING Signal peptide predictions WAITING Annotations blast2GO WAITING View results Internet Protected Mode On Figure 3 Cancel a request Web Page of ArthropodEST pipeline system 3 1 4 View Request Results When results are ready the system will send a notification email with a link to a web page where the user can download the results of the completed analysis It is important to notice that depending on the options that the user selected to perform the analysis the system may send two emails notifying the results This is because the system
14. el it using the Analysis Request Detail Web Page As is shown Figure 10 a Cancel Request button will be displayed and after pressing the button a message will appear so that Administrator confirms the intention to cancel the request After cancelling a notification will be sent to user indicating that the request was successfully cancelled File Edit View History Bookmarks Tools Help e x 4 E hipy12913011577 e2 beocat admin viewjob php id 1 ArthropodEST K State Bioinformatics EST analysis pipeline Logout Change Pass Resources Reports Request Input File s ee sees EIET benchmark500 seq 257984 me poo meer pe moun arguments d arthropodest tmp myproject loBEdcjzsoKs o arthropodest Ir myproject loBEdcjzsoKs e info ecuadorhost com P myproject F benchmark500 seq S l 100 V r drosophila A 1 t p 94 1 30 v 600 O c 12 4 20 o 40 p 90 s 900 y 100 h 20 300 z 3 p 1 B 1 Refresh information Cancel EST analysis CC eo sms sanne Eine ESE EX ws foe Eo wee mess le sro armo amare ca Figure 10 Cancel Request Administration Interface Page 26 User Manual Version 1 0 3 2 8 View Request Results Also on Analysis Request Detail Web Page if results are ready to download a link in the bottom of the page will allow users to open the Results Web Page A screen shot is shown in Figure 4 3 2 9 Start and Stop Engine coo
15. g ramiko messages handler fileHandler args STRING tmp est log Engine file handler Specify the log file path for the a main application messages handler fileHandler args STRING tmp parami Paramiko Library file handler Define log file path for _paramiko ko log a paramiko library s messages e Table 2 Configuration file engine logging cfg 2 1 4 Web Interface The web interface will content the web pages to interact with user and administrator To install the web interface the following steps needs to be done e Unpack the web pages source code in a folder with permissions access for apache user e Configure the folder as a virtual directory using apache configuration manual e Edit admin config php file and configure the following lines of code to be able to connect ArthropodEST MySQL database Page 10 User Manual Version 1 0 Sdatabase arthropodest Suser arthropodest Spass arthropodestpass Shost dbhostname Sport 3306 e Edit e pl file and configure the following lines of code in its header with appropriate values DATABASE Section my Sdb arthropodest my Shost localhost my Sport 3306 my Sdbuser arthropodest my Sdbpass arthropodestpass GENERAL Section my SURL http 129 130 115 77 e2 beocat my SREMOTE_EST_FOLDER arthropodest my SLOCAL_EST_UPLOAD_DIR tmp e2 beoca
16. he time out configuration can be done on section sessions on etc php ini file 3 2 3 Change Password Page 20 User Manual Version 1 0 This Web Page is intended to change the password for the administrator He or she needs to enter the old password and the new password twice The following figure shows the interface for changing password admin ArthropodEST Change Pa pS Aa GU w Favorites ao R Arthropo Ka Arthr X ArthropodEST K State Bioinformatics EST analysis pipeline Logout Change Pass Resources Reports Change Password Old Password New Password Confirm Password Internet Protected Mode On Figure 6 Change Password Web Page Administration Interface 3 2 4 Resources This Web Page allows administrator to configure how the engine scheduler will allocate resources to requests The key factor will be the number of sequences to be analyzed on an input file The scheduler will scan the resource records from the smallest sequence value to the largest one until it finds the correspondent match for a particular request For every request there must be 3 records corresponding to the 3 pipeline scripts that can be executed on Beocat Before allocating the number of CPUs amount of memory and hours for a particular execution the engine will count the number of currently executions running and compute the percentage of charge according the maximum executions Page 21
17. il s that will be blind carbon copied for all the notifications to users General fileParameters STRING arguments File name that will content the arguments built by web page request e pl wwwUploadBaseDir STRING tmp www_e Local folder where apache will upload the input files of requests remoteFolder STRING arthropodest Name of remote folder on Beocat where the pipeline components where installed localFolder STRING var www e Local folder where the web pages for user requests are located jobScript1 STRING job e seqcl repmask sh Path where the script to run job 1 is located on Beocat sequence cleaner repmasker and cap3 executions jobScript2 STRING job e signalp sh Path where the script to run job 2 is located on Beocat signal executions jobScript3 STRING job e blast2go sh Path where the script to run job 3 is located on Beocat blast2go executions email_ack STRING email_ack File name that will content the email content that will be built by web page request e pl urlHost STRING http 129 13 0 115 77 e Base URL where the web interface can be browsed timeMonitor INT 5 Seconds for the frequency that the engine will process the queue totalRuns STRING var www e log total_run S Path to the file that will content the number of total requests processed by the system
18. n of the configuration file of the main engine application Section Parameter Name Format Default Example Description MySql host STRING localhost Database host name might be IP address port INT 3306 Database connection port user STRING dbuser Database user name password STRING dbpassword Database password db STRING dbname Database name e Table 3 Configuration file log est cfg 2 2 2 Bioinformatics Software Bioinformatics programs must be installed and able to run on Beocat user account The necessary packages which are launched from pipeline scripts and need to be installed are listed below e TGICL software e SeqClean e NCBI BLAST suite Page 12 User Manual Version 1 0 Vectors databases e RepeatMasker software including Tandem Repeats Finder Repeat Database cross match e CAP3 e Blast2Go e Signal e EMBOSS 2 2 3 Pipeline scripts The pipeline scripts are the main code to perform the EST analysis They will execute the Bioinformatics Software and Event Log component previously installed The following are the steps to set up the Pipeline scripts Beocat account user must perform the installation e Unpack the pipeline scripts source code in a sub folder of Beocat account user e Grant read and write permissions only Beocat account user e Make the modifications on the configuration file ArthropodEST conf sh to determine where the bioinformatics
19. nalysis and correspondent Bioinformatics Software It is expected that users have knowledge of the EST pipeline analysis process This manually simply explains the operation of ArhtorpodEST Pipeline software components and does not go into details about the bioinformatics processing activities 2 Installation and Configuration ArthropodEST Pipeline is a distributed system that needs different components to be installed over two main servers Bioinformatics Center BC and Beocat Cluster Server refer to Architecture Design document section 2 1 for more information on physical distribution 2 1 Bioinformatics Server The following components of ArthropodEST pipeline system will be installed on this server e Database The centric information repository of the Pipeline system e User Interface Web pages to interact with users e Engine component Coordinator to manage and processes requests 2 1 1 Required Software e GNU Linux Ubuntu Server 8 04 or superior Page 6 User Manual Version 1 0 2 1 2 MySQL 5 0 or superior Python 2 6 including python mysqldb pycryto paramiko libraries Perl 5 0 including CGI File Temp DBI DBD mysql libraries Php 5 0 including php5 mysal library Apache 2 2 including mod perl mod php add ins Database The main system database use MySQL as Relational Database Engine The rest of components will need to set up a connection configuration string according where this database will be mounted
20. o software tgi bioinfo software tgi tgicl linux bioinfo software tgi tgicl linux bin bioinfo software tgi s eqclean bioinfo software tgi seqclean bin bioinfo software ncbi blast bin bioinfo software ncbi blast netblast bin bioinfo software wu blast bioinfo software RepeatMasker bioinfo software cap3 bioinfo softwar e pcap rep bioinfo software phred phrap consed bioinfo software signalp b ioinfo software blast2go bioinfo software GFF3 Validator bioinfo software EMBOSS bin arthropodest bin bin export PATH S PATH SArthropodEST PATH 3 ArthropodEST Pipeline Usage 3 1 User Interface Page 14 User Manual Version 1 0 The purpose of this section is to provide a reference how a user must interact with the ArthropodEST Pipeline system to perform analysis requests 3 1 1 Submit a Request User should open the request web page inside a browser using the appropriate URL For example http arthropodest bioinformatics ksu edu e beocat The following screen will be displayed alysis pipeline Windows Internet Explore EPI X f ArthropodEST Job MME kb Page Safetyv Tock Gr ArthropodEST K State Bioinformatics EST analysis pipeline About the pipeline Example runs with benchmark10000 seg default parameters with without TGICL clustering 84 projects completed to date since Jan 3 2008 Project name required Your email address required my project luisc ksu edu
21. quests that have been placed and processed by the ArthropodEST Pipeline System The header provides different Page 22 User Manual Version 1 0 alternatives to filter the search The footer provides navigation for the pagination of the list of analysis requests Figure 8 shows how a report looks like including the table that lists the analysis requests with the main information To review the complete information of a specific analysis request the administrator can select the link view at the right of every request The possible filters to search requests are Job ID job identifier assigned by Beocat project name user email status CREATED CANCELLED SUBMITTED STOPPED DONE ERROR and range of dates when requests were placed Page 23 User Manual Version 1 0 Q VERSES MOTRIN Safety v med ArthropodEST K State Bioinformatics EST analysis pipeline Logout Change Pass Resources Reports JobID Project Name Email to format mm dd yyyy 5 Project Date Email test1 april15 04 15 2010 16 48 01 DONE info ecuadorhost com test2 april15 04 15 2010 19 33 47 DONE info ecuadorhost com test2 april15 04 15 2010 20 33 46 DONE info ecuadorhost com test3 april15 04 15 2010 21 00 50 DONE info ecuadorhost com test4 april15 04 15 2010 21 08 18 DONE info ecuadorhost com test5 april15
22. rdinator After the installation and configuration of ArthropodEST Pipeline system the administrator must run apache web server on BC Server and MySQL before starting the engine component The command to start the engine component service is as follows python path to engine engin st py start The command to stop the service is as follows python path to engine engin st py stop The command to restart the service is as follows python path to engine engin st py restart Page 27
23. res Figure 1 Request submission Web Page of ArthropodEST pipeline system 16 Figure 2 Monitor a request Web Page of ArthropodEST pipeline system 17 Figure 3 Cancel a request Web Page of ArthropodEST pipeline system esee 18 Figure 4 Results Web Page of ArthropodEST pipeline system 19 Figure 5 Login Web Page Administration Interface ccccccccccccssssssscececessessaececcesceeseseeaeeeecesseseaeseeeeseesees 20 Figure 6 Change Password Web Page Administration Interface 21 Figure 7 Resource Web Page Administration Interface 22 Figure 8 Reports Web Page Administration Interface 24 Figure 9 Request Detail Web Page Administration Interface esses enne 25 Figure 10 Cancel Request Administration Interface eene ennemis sn nnne 26 Table of Tables e Table 1 Configuration file engine est ce e Table 2 Configuration file engine Jogging ce e Table 3 Configuration file log est cfg User Manual Version 1 0 1 Introduction This document provides a user manual for ArthorpodEST Pipeline System It is divided in two sections Installation and Configuration and System Usage The first section describes the components to be installed and the possible configurations supported The next section Usage describes how to interact with the system from the user and administrator perspective The intention of this manual is to guide experienced researchers and technicians familiar with expressed sequence tag EST a
24. t ANTIVIRUS Section my SCLAMSCAN usr bin clamscan my SCLAMSCAN OPT quiet e Edit e cgi file and configure the following lines of code in its header with appropriate values TOTAL RUNS FILE var www e2 beocat log total runs QUEUE LENGTH FILE var www e2 beocat log queue length Notice that most of the variable values are the same as the main engine configuration file Those variable values should match in order to execute the components 2 2 Beocat Cluster Server The following components of ArthropodEST pipeline system will be installed on this server Page 11 User Manual Version 1 0 e Event log component to keep track of errors and status of analysis execution e Pipeline scripts to perform the analysis requests e Bioinformatics software 2 2 1 Event Log component This component allows the interaction between pipeline scripts on Beocat and main engine coordinator on BC Server It is a script developed in python The following are the steps to set up the Event log script Beocat account user must perform the installation e Unpack the Event log source code in a sub folder of Beocat account user e Grant read and write permissions to configuration files to only Beocat account user e Make the modifications on the configuration file log est cfg to communicate with the main System Database on BC Server according to table below Notice that the configuration file is a small versio
25. will execute the analysis in two phases and after each of them it will Page 18 User Manual Version 1 0 retrieve the results from Beocat and send the notification to the User The options for first phase are the Bioinformatics Programs Sequence cleaner repmasker and CAP3 On second phase Blast2go and signal Peptides predictions are executed Finally on monitor status Web Page if results are ready to download a link in the bottom of the page will allow users to open the same Results Web Page The following is an example of result page my e R http 129 130 115 77 e2 beocat r myprojecttiny Mn7L v BEA sik Favorites f Index of e2 beocat t myprojecttiny Mn7UU Index of e2 beocat r myprojecttiny Mn7UUQT6UZ8v Name Last modified Size Description myprojecttiny report txt 21 Apr 2010 0021 3 6K ON pea aphid ests raw txt clean gz 21 Apr 2010 00 21 1 2K P ea aphid ests raw txt clean masked cap ace gz 21 Apr 2010 00 21 1 3K dh pea aphid ests raw txt clean masked cap align 21 Apr 2010 00 21 1 3K P pea aphid ests raw txt clean masked cap contigs contigs distribution gz 21 Apr 2010 0021 126 P pea aphid ests raw txt clean masked cap contigs contigs tbl gz 21 Apr 2010 0021 240 ON pea aphid ests raw txt clean masked cap contigs gz 21 Apr 2010 00 21 586 P ea aphid ests raw txt clean masked cap contigs qual 21 Apr 2010 0021 194 ON pea aphid ests raw txt clean masked cap info txt gz 21 Apr 2010 00 21 368 P pea
26. word to decrypt it must be defined here SMTP Server Server STRING localhost SMTP server host name might be IP address Port INT 587 SMTP server port number Email STRING user localho st com User login name for SMTP server Must be defined if server requires authentication password STRING User password for SMTP server Must be defined if server requires authentication Scheduler maxConcurrentJobs INT Number of maximum allowed executions that can run concurrently on Beocat Page 8 User Manual Version 1 0 maxCpus Number of maximum allowed cpus that can be used concurrently on Beocat threshold Percentage of simultaneous executions on Beocat that need to be overcome before using the minimum resources to allocate new executions Otherwise the maximum resources will be allocated for each execution Refer resource administration on usage section maxCpusPerJob Number of maximum cpus that can be used per each execution on Beocat This must match the maximum number of cpus that one node on Beocat supports Executions cannot share cpus from different nodes Mail Recipients sender STRING bioinfo ksu edu Email of the sender of notification emails admin STRING me ksu edu Administrator email s cc STRING Email s that will be carbon copied for all the notifications to users bcc STRING Ema
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